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- PDB-2btp: 14-3-3 Protein Theta (Human) Complexed to Peptide -

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Basic information

Entry
Database: PDB / ID: 2btp
Title14-3-3 Protein Theta (Human) Complexed to Peptide
Components
  • 14-3-3 PROTEIN TAU
  • CONSENSUS PEPTIDE FOR 14-3-3 PROTEINS
KeywordsSIGNALING PROTEIN/PEPTIDE / 14-3-3 / PHOSPHOSERINE / STRUCTURAL GENOMICS CONSORTIUM / PHOSPHORYLATION / COMPLEX (SIGNAL TRANSDUCTION-PEPTIDE) / SIGNALING PROTEIN-PEPTIDE complex
Function / homology
Function and homology information


negative regulation of monoatomic ion transmembrane transport / small GTPase-mediated signal transduction / Regulation of localization of FOXO transcription factors / Activation of BAD and translocation to mitochondria / protein targeting / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / 14-3-3 protein binding ...negative regulation of monoatomic ion transmembrane transport / small GTPase-mediated signal transduction / Regulation of localization of FOXO transcription factors / Activation of BAD and translocation to mitochondria / protein targeting / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / 14-3-3 protein binding / substantia nigra development / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / intracellular protein localization / transmembrane transporter binding / protein domain specific binding / focal adhesion / negative regulation of DNA-templated transcription / synapse / signal transduction / protein-containing complex / extracellular exosome / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
14-3-3 theta / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily ...14-3-3 theta / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
14-3-3 protein theta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsElkins, J.M. / Johansson, A.C.E. / Smee, C. / Yang, X. / Sundstrom, M. / Edwards, A. / Arrowsmith, C. / Doyle, D.A. / Structural Genomics Consortium (SGC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: Structural Basis for Protein-Protein Interactions in the 14-3-3 Protein Family.
Authors: Yang, X. / Lee, W.H. / Sobott, F. / Papagrigoriou, E. / Robinson, C.V. / Grossmann, J.G. / Sundstrom, M. / Doyle, D.A. / Elkins, J.M.
History
DepositionJun 5, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 24, 2017Group: Structure summary
Revision 1.4Jan 31, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.5Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.6Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.7Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 PROTEIN TAU
B: 14-3-3 PROTEIN TAU
P: CONSENSUS PEPTIDE FOR 14-3-3 PROTEINS
Q: CONSENSUS PEPTIDE FOR 14-3-3 PROTEINS


Theoretical massNumber of molelcules
Total (without water)60,0614
Polymers60,0614
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)61.307, 85.964, 64.666
Angle α, β, γ (deg.)90.00, 112.67, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12P
22Q

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 230
2111B1 - 230
1123P1 - 7
2123Q1 - 7

NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (-0.98666, -0.16262, -0.00741), (-0.16258, 0.98207, 0.09542), (-0.00824, 0.09535, -0.99541)
Vector: 2.04291, 1.21412, -23.69813)
DetailsTHE ENTRY IS MARKED TETRAMERIC SINCE THE CHAINS AAND B ARE BOUND TO PEPTIDES P AND Q. THE PROTEINITSELF IS DIMERIC IN NATURE.

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Components

#1: Protein 14-3-3 PROTEIN TAU / 14-3-3 PROTEIN THETA / 14-3-3 PROTEIN T-CELL / HS1 PROTEIN


Mass: 29234.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: THE MAMMALIAN GENE COLLECTION, I.M.A.G.E. CONSORTIUM CLONEID 6164592
Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: P27348
#2: Protein/peptide CONSENSUS PEPTIDE FOR 14-3-3 PROTEINS


Mass: 795.781 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: PHOSPHOSERINE AT RESIDUES P 5 AND Q 5 / Source: (synth.) HOMO SAPIENS (human)
Compound detailsFUNCTION: STRONGLY ACTIVATES PROTEIN KINASE C
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54 %
Crystal growpH: 8.5
Details: 0.2M SODIUM ACETATE TRIHYDRATE, 0.1M TRISHCL PH8.5,30% PEG4000, pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU-MSC R-AXIS HTC / Detector: IMAGE PLATE / Date: May 21, 2005 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→34.88 Å / Num. obs: 14743 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.7
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.5 / % possible all: 93.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QJA

1qja


Resolution: 2.8→59.66 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.905 / SU B: 29.994 / SU ML: 0.266 / Cross valid method: THROUGHOUT / ESU R Free: 0.395 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1121 7.6 %RANDOM
Rwork0.206 ---
obs0.21 13606 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.01 Å20 Å2-0.45 Å2
2--3.62 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 2.8→59.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3727 0 0 0 3727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223782
X-RAY DIFFRACTIONr_bond_other_d0.0020.023427
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.9645129
X-RAY DIFFRACTIONr_angle_other_deg0.83937923
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3325474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.09924.773176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.87815.047639
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4451522
X-RAY DIFFRACTIONr_chiral_restr0.0780.2595
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024225
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02745
X-RAY DIFFRACTIONr_nbd_refined0.2520.2934
X-RAY DIFFRACTIONr_nbd_other0.1720.23282
X-RAY DIFFRACTIONr_nbtor_refined0.1950.21939
X-RAY DIFFRACTIONr_nbtor_other0.0930.22166
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.277
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2880.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5411.52576
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.83623816
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3131517
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1064.51313
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3172tight positional0.030.05
2P34tight positional0.040.05
2P34loose positional0.335
1A3172tight thermal0.220.5
2P34tight thermal0.080.5
2P34loose thermal1.3610
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.352 78
Rwork0.325 954
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.4169-0.80060.70421.7351-0.44612.0629-0.01580.1178-0.06990.09420.05990.0849-0.01810.0131-0.044-0.0886-0.0351-0.0232-0.2159-0.0375-0.1514-12.4285-13.7369-24.6921
21.66330.48811.26741.55421.10613.52410.0176-0.0771-0.1216-0.06460.0155-0.134-0.04230.0344-0.033-0.10870.0174-0.0124-0.0690.0117-0.092215.3968-13.7638-0.7488
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-18 - 230
2X-RAY DIFFRACTION2B1 - 230

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